here is one suggestion...!just try it this way...I am pretty sure its gonna work for you...!
make a 2 division
<div>
blah blah.....thsi is your main control...like gridview, tabs, buttons anything(which is on main screen)
</div>
now in another division
<div >
make a panel with all control you wanna show when popup show up...Like labels, textbox etc....
<panel id="xyz" cssclass = "popup">
controls
</panel>
<ajax:modalpopupextender .....with properties....>
</ajax:modapopupextender>
</div>
now in css you can do anything you want in cssclass .popup...!
Regards,
Varun Jaswal.